scholarly journals Massive gene presence/absence variation in the mussel genome as an adaptive strategy: first evidence of a pan-genome in Metazoa

2019 ◽  
Author(s):  
Marco Gerdol ◽  
Rebeca Moreira ◽  
Fernando Cruz ◽  
Jessica Gómez-Garrido ◽  
Anna Vlasova ◽  
...  
Keyword(s):  
Large Scale ◽  
Single Copy ◽  
Genomic Diversity ◽  
Small Scale ◽  
Nucleotide Polymorphisms ◽  
Structural Variations ◽  
Pan Genome ◽  
Adaptive Value ◽  
Mediterranean Mussel ◽  
The Mediterranean

AbstractMussels are ecologically and economically relevant edible marine bivalves, highly invasive and resilient to biotic and abiotic stressors causing recurrent massive mortalities in other species. Here we show that the Mediterranean mussel Mytilus galloprovincialis has a complex pan-genomic architecture, which includes a core set of 45,000 genes shared by all individuals plus a surprisingly high number of dispensable genes (∼15,000). The latter are subject to presence/absence variation (PAV), i.e., they may be entirely missing in a given individual and, when present, they are frequently found as a single copy. The enrichment of dispensable genes in survival functions suggests an adaptive value for PAV, which might be the key to explain the extraordinary capabilities of adaptation and invasiveness of this species. Our study underpins a unique metazoan pan-genome architecture only previously described in prokaryotes and in a few non-metazoan eukaryotes, but that might also characterize other marine invertebrates.Significance statementIn animals, intraspecific genomic diversity is generally thought to derive from relatively small-scale variants, such as single nucleotide polymorphisms, small indels, duplications, inversions and translocations. On the other hand, large-scale structural variations which involve the loss of genomic regions encoding protein-coding genes in some individuals (i.e. presence/absence variation, PAV) have been so far only described in bacteria and, occasionally, in plants and fungi. Here we report the first evidence of a pan-genome in the animal kingdom, revealing that 25% of the genes of the Mediterranean mussel are subject to PAV. We show that this unique feature might have an adaptive value, due to the involvement of dispensable genes in functions related with defense and survival.

scholarly journals Whole genome sequencing reveals the genomic diversity, taxonomic classification, and evolutionary relationships of the genus Nocardia

2021 ◽  
Vol 15 (8) ◽  
pp. e0009665
Author(s):  
Shuai Xu ◽  
Zhenpeng Li ◽  
Yuanming Huang ◽  
Lichao Han ◽  
Yanlin Che ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Trees ◽  
Gene Families ◽  
Single Copy ◽  
Taxonomic Classification ◽  
Genomic Diversity ◽  
Evolutionary Relationships ◽  
Taxonomic Structure ◽  
Pan Genome ◽  
Dipeptidyl Aminopeptidase

Nocardia is a complex and diverse genus of aerobic actinomycetes that cause complex clinical presentations, which are difficult to diagnose due to being misunderstood. To date, the genetic diversity, evolution, and taxonomic structure of the genus Nocardia are still unclear. In this study, we investigated the pan-genome of 86 Nocardia type strains to clarify their genetic diversity. Our study revealed an open pan-genome for Nocardia containing 265,836 gene families, with about 99.7% of the pan-genome being variable. Horizontal gene transfer appears to have been an important evolutionary driver of genetic diversity shaping the Nocardia genome and may have caused historical taxonomic confusion from other taxa (primarily Rhodococcus, Skermania, Aldersonia, and Mycobacterium). Based on single-copy gene families, we established a high-accuracy phylogenomic approach for Nocardia using 229 genome sequences. Furthermore, we found 28 potentially new species and reclassified 16 strains. Finally, by comparing the topology between a phylogenomic tree and 384 phylogenetic trees (from 384 single-copy genes from the core genome), we identified a novel locus for inferring the phylogeny of this genus. The dapb1 gene, which encodes dipeptidyl aminopeptidase BI, was far superior to commonly used markers for Nocardia and yielded a topology almost identical to that of genome-based phylogeny. In conclusion, the present study provides insights into the genetic diversity, contributes a robust framework for the taxonomic classification, and elucidates the evolutionary relationships of Nocardia. This framework should facilitate the development of rapid tests for the species identification of highly variable species and has given new insight into the behavior of this genus.

scholarly journals Sinking microplastics in the water column: simulations in the Mediterranean Sea

Ocean Science ◽  
2021 ◽  
Vol 17 (2) ◽  
pp. 431-453
Author(s):  
Rebeca de la Fuente ◽  
Gábor Drótos ◽  
Emilio Hernández-García ◽  
Cristóbal López ◽  
Erik van Sebille
Keyword(s):  
Vertical Distribution ◽  
Mediterranean Sea ◽  
Water Column ◽  
Large Scale ◽  
Circulation Model ◽  
Small Scale ◽  
The Mediterranean ◽  
Scale Turbulence ◽  
Non Gaussian ◽  
The Vertical Distribution

Abstract. We study the vertical dispersion and distribution of negatively buoyant rigid microplastics within a realistic circulation model of the Mediterranean sea. We first propose an equation describing their idealized dynamics. In that framework, we evaluate the importance of some relevant physical effects (inertia, Coriolis force, small-scale turbulence and variable seawater density), and we bound the relative error of simplifying the dynamics to a constant sinking velocity added to a large-scale velocity field. We then calculate the amount and vertical distribution of microplastic particles on the water column of the open ocean if their release from the sea surface is continuous at rates compatible with observations in the Mediterranean. The vertical distribution is found to be almost uniform with depth for the majority of our parameter range. Transient distributions from flash releases reveal a non-Gaussian character of the dispersion and various diffusion laws, both normal and anomalous. The origin of these behaviors is explored in terms of horizontal and vertical flow organization.

scholarly journals Chromosome-level assembly of Arabidopsis thaliana Ler reveals the extent of translocation and inversion polymorphisms

2016 ◽  
Vol 113 (28) ◽  
pp. E4052-E4060 ◽  
Author(s):  
Luis Zapata ◽  
Jia Ding ◽  
Eva-Maria Willing ◽  
Benjamin Hartwig ◽  
Daniela Bezdan ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Meiotic Recombination ◽  
Large Scale ◽  
Local Variation ◽  
Single Copy ◽  
Reference Sequence ◽  
Genome Comparison ◽  
Small Scale ◽  
Worldwide Population ◽  
Linkage Information

Resequencing or reference-based assemblies reveal large parts of the small-scale sequence variation. However, they typically fail to separate such local variation into colinear and rearranged variation, because they usually do not recover the complement of large-scale rearrangements, including transpositions and inversions. Besides the availability of hundreds of genomes of diverse Arabidopsis thaliana accessions, there is so far only one full-length assembled genome: the reference sequence. We have assembled 117 Mb of the A. thaliana Landsberg erecta (Ler) genome into five chromosome-equivalent sequences using a combination of short Illumina reads, long PacBio reads, and linkage information. Whole-genome comparison against the reference sequence revealed 564 transpositions and 47 inversions comprising ∼3.6 Mb, in addition to 4.1 Mb of nonreference sequence, mostly originating from duplications. Although rearranged regions are not different in local divergence from colinear regions, they are drastically depleted for meiotic recombination in heterozygotes. Using a 1.2-Mb inversion as an example, we show that such rearrangement-mediated reduction of meiotic recombination can lead to genetically isolated haplotypes in the worldwide population of A. thaliana. Moreover, we found 105 single-copy genes, which were only present in the reference sequence or the Ler assembly, and 334 single-copy orthologs, which showed an additional copy in only one of the genomes. To our knowledge, this work gives first insights into the degree and type of variation, which will be revealed once complete assemblies will replace resequencing or other reference-dependent methods.

scholarly journals Chloroplast Genome Sequencing, Comparative Analysis, and Discovery of Unique Cytoplasmic Variants in Pomegranate (Punica granatum L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Nripendra Vikram Singh ◽  
Prakash Goudappa Patil ◽  
Roopa P. Sowjanya ◽  
Shilpa Parashuram ◽  
Purushothaman Natarajan ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Large Scale ◽  
Punica Granatum ◽  
Single Copy ◽  
Structural Variations ◽  
Phylogenetic Studies ◽  
Cp Genome ◽  
Next Generation Sequencing Ngs ◽  
Contraction And Expansion ◽  
Chloroplast Genome Sequencing

Here we report on comprehensive chloroplast (cp) genome analysis of 16 pomegranate (Punica granatum L.) genotypes representing commercial cultivars, ornamental and wild types, through large-scale sequencing and assembling using next-generation sequencing (NGS) technology. Comparative genome analysis revealed that the size of cp genomes varied from 158,593 bp (in wild, “1201” and “1181”) to 158,662 bp (cultivar, “Gul-e-Shah Red”) among the genotypes, with characteristic quadripartite structures separated by a pair of inverted repeats (IRs). The higher conservation for the total number of coding and non-coding genes (rRNA and tRNA) and their sizes, and IRs (IR-A and IR-B) were observed across all the cp genomes. Interestingly, high variations were observed in sizes of large single copy (LSC, 88,976 to 89,044 bp) and small single copy (SSC, 18,682 to 18,684 bp) regions. Although, the structural organization of newly assembled cp genomes were comparable to that of previously reported cp genomes of pomegranate (“Helow,” “Tunisia,” and “Bhagawa”), the striking differences were observed with the Lagerstroemia lines, viz., Lagerstroemia intermedia (NC_0346620) and Lagerstroemia speciosa (NC_031414), which clearly confirmed previous findings. Furthermore, phylogenetic analysis also revealed that members outside the genus Punica were clubbed into a separate clade. The contraction and expansion analysis revealed that the structural variations in IRs, LSC, and SSC have significantly accounted for the evolution of cp genomes of Punica and L. intermedia over the periods. Microsatellite survey across cp genomes resulted in the identification of a total of 233 to 234 SSRs, with majority of them being mono- (A/T or C/G, 164–165 numbers), followed by di- (AT/AT or AG/CT, 54), tri- (6), tetra- (8), and pentanucleotides (1). Furthermore, the comparative structural variant analyses across cp genomes resulted in the identification of many varietal specific SNP/indel markers. In summary, our study has offered a successful development of large-scale cp genomics resources to leverage future genetic, taxonomical, and phylogenetic studies in pomegranate.

Genetics of rheumatoid arthritis

2013 ◽  
Author(s):  
Steve Eyre ◽  
Jane Worthington
Keyword(s):  
Rheumatoid Arthritis ◽  
Large Scale ◽  
Association Studies ◽  
Epidemiological Studies ◽  
Convincing Evidence ◽  
Susceptibility Locus ◽  
Small Scale ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Hla Association

A range of epidemiological studies have clearly established that susceptibility to rheumatoid arthritis (RA) is determined by both genetic and environmental factors. Studies over the last five decades have used a variety of approaches to identify the genetic variants associated with disease. HLA DRB1 was the first RA susceptibility locus to be discovered and has the largest effect size. We describe current understanding of the complexities of HLA association for RA. Linkage and small-scale association studies prior to 2007 provided convincing evidence for only one more RA susceptibility locus, PTPN22. Major breakthroughs in high-throughput genotyping and systematic discovery and mapping of hundreds of thousands of single nucleotide polymorphisms (SNPs) led to large-scale genome-wide association studies used for the first time for RA in 2007. This approach has had a dramatic impact on our knowledge of the susceptibility loci for RA, such that over 60 risk variants have now been robustly identified. We present an overview of these studies and the loci that have been identified. We consider how this knowledge is contributing to a greater understanding of the aetiology and pathology of the disease and in turn how this can influence management of patients presenting with an inflammatory arthritis. We consider some of the unanswered questions and the approaches that will need to be taken to address them.

scholarly journals Human Genomic Diversity Where the Mediterranean Joins the Atlantic

2019 ◽  
Vol 37 (4) ◽  
pp. 1041-1055 ◽  
Author(s):  
Candela L Hernández ◽  
Guillermo Pita ◽  
Bruno Cavadas ◽  
Saioa López ◽  
Luis J Sánchez-Martínez ◽  
...  
Keyword(s):  
Iberian Peninsula ◽  
African Ancestry ◽  
Mediterranean Area ◽  
Western Mediterranean ◽  
Genomic Diversity ◽  
Nucleotide Polymorphisms ◽  
Present Contribution ◽  
Southern Portugal ◽  
Human Genomic ◽  
The Mediterranean

Abstract Throughout the past few years, a lively debate emerged about the timing and magnitude of the human migrations between the Iberian Peninsula and the Maghreb. Several pieces of evidence, including archaeological, anthropological, historical, and genetic data, have pointed to a complex and intermingled evolutionary history in the western Mediterranean area. To study to what extent connections across the Strait of Gibraltar and surrounding areas have shaped the present-day genomic diversity of its populations, we have performed a screening of 2.5 million single-nucleotide polymorphisms in 142 samples from southern Spain, southern Portugal, and Morocco. We built comprehensive data sets of the studied area and we implemented multistep bioinformatic approaches to assess population structure, demographic histories, and admixture dynamics. Both local and global ancestry inference showed an internal substructure in the Iberian Peninsula, mainly linked to a differential African ancestry. Western Iberia, from southern Portugal to Galicia, constituted an independent cluster within Iberia characterized by an enriched African genomic input. Migration time modeling showed recent historic dates for the admixture events occurring both in Iberia and in the North of Africa. However, an integrative vision of both paleogenomic and modern DNA data allowed us to detect chronological transitions and population turnovers that could be the result of transcontinental migrations dating back from Neolithic times. The present contribution aimed to fill the gaps in the modern human genomic record of a key geographic area, where the Mediterranean and the Atlantic come together.

scholarly journals Advances in understanding the evolution of fungal genome architecture

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 776 ◽  
Author(s):  
Shelby J. Priest ◽  
Vikas Yadav ◽  
Joseph Heitman
Keyword(s):  
Large Scale ◽  
High Throughput Sequencing ◽  
Rapid Evolution ◽  
Genomic Diversity ◽  
Fungal Genome ◽  
Small Scale ◽  
Genomic Changes ◽  
Wide Range ◽  
Domains Of Life ◽  
Fungal Genomes

Diversity within the fungal kingdom is evident from the wide range of morphologies fungi display as well as the various ecological roles and industrial purposes they serve. Technological advances, particularly in long-read sequencing, coupled with the increasing efficiency and decreasing costs across sequencing platforms have enabled robust characterization of fungal genomes. These sequencing efforts continue to reveal the rampant diversity in fungi at the genome level. Here, we discuss studies that have furthered our understanding of fungal genetic diversity and genomic evolution. These studies revealed the presence of both small-scale and large-scale genomic changes. In fungi, research has recently focused on many small-scale changes, such as how hypermutation and allelic transmission impact genome evolution as well as how and why a few specific genomic regions are more susceptible to rapid evolution than others. High-throughput sequencing of a diverse set of fungal genomes has also illuminated the frequency, mechanisms, and impacts of large-scale changes, which include chromosome structural variation and changes in chromosome number, such as aneuploidy, polyploidy, and the presence of supernumerary chromosomes. The studies discussed herein have provided great insight into how the architecture of the fungal genome varies within species and across the kingdom and how modern fungi may have evolved from the last common fungal ancestor and might also pave the way for understanding how genomic diversity has evolved in all domains of life.

scholarly journals Sinking microplastics in the water column: simulations in the Mediterranean Sea

2020 ◽  
Author(s):  
Rebeca de la Fuente ◽  
Gábor Drótos ◽  
Emilio Hernández García ◽  
Cristóbal López ◽  
Erik van Sebille
Keyword(s):  
Vertical Distribution ◽  
Mediterranean Sea ◽  
Water Column ◽  
Large Scale ◽  
Circulation Model ◽  
Small Scale ◽  
The Mediterranean ◽  
Scale Turbulence ◽  
Non Gaussian ◽  
The Vertical Distribution

Abstract. We study the vertical dispersion and distribution of negatively buoyant rigid microplastics within a realistic circulation model of the Mediterranean sea. We first propose an equation describing their idealized dynamics. In that framework, we evaluate the importance of some relevant physical effects: inertia, Coriolis force, small-scale turbulence and variable seawater density, and bound the relative error of simplifying the dynamics to a constant sinking velocity added to a large-scale velocity field. We then calculate the amount and vertical distribution of microplastic particles on the water column of the open ocean if their release from the sea surface is continuous at rates compatible with observations in the Mediterranean. The vertical distribution is found to be almost uniform with depth for the majority of our parameter range. Transient distributions from flash releases reveal a non-Gaussian character of the dispersion and various diffusion laws, both normal and anomalous. The origin of these behaviors is explored in terms of horizontal and vertical flow organization.

scholarly journals Sinking microplastics in the water column: simulations in the Mediterranean Sea

2021 ◽  
Author(s):  
Rebeca de la Fuente ◽  
Gábor Drótos ◽  
Emilio Hernández ◽  
Cristóbal López ◽  
Erik van Sebille
Keyword(s):  
Vertical Distribution ◽  
Mediterranean Sea ◽  
Water Column ◽  
Large Scale ◽  
Circulation Model ◽  
Small Scale ◽  
The Mediterranean ◽  
Scale Turbulence ◽  
Non Gaussian ◽  
The Vertical Distribution

<p>We study the vertical dispersion and distribution of negatively buoyant rigid microplastics within a realistic circulation model of the Mediterranean sea. We first propose an equation describing their idealized dynamics. In that framework, we evaluate the importance of some relevant physical effects: inertia, Coriolis force, small-scale turbulence and variable seawater density, and bound the relative error of simplifying the dynamics to a constant sinking velocity added to a large-scale velocity field. We then calculate the amount and vertical distribution of microplastic particles on the water column of the open ocean if their release from the sea surface is continuous at rates compatible with observations in the Mediterranean. The vertical distribution is found to be almost uniform with depth for the majority of our parameter range. Transient distributions from flash releases reveal a non-Gaussian character of the dispersion and various diffusion laws, both normal and anomalous. The origin of these behaviors is explored in terms of horizontal and vertical flow organization.</p>

Genetics of rheumatoid arthritis

2013 ◽  
pp. 308-312
Author(s):  
Steve Eyre ◽  
Gisela Orozco ◽  
Jane Worthington
Keyword(s):  
Rheumatoid Arthritis ◽  
Large Scale ◽  
Association Studies ◽  
Epidemiological Studies ◽  
Convincing Evidence ◽  
Susceptibility Locus ◽  
Small Scale ◽  
Nucleotide Polymorphisms ◽  
Risk Variants ◽  
Genetic And Environmental Factors

A range of epidemiological studies have clearly established that susceptibility to rheumatoid arthritis (RA) is determined by both genetic and environmental factors. Studies over the last five decades have used a variety of approaches to identify the genetic variants associated with disease. HLA-DRB1 was the first RA susceptibility locus to be discovered and has the largest effect size. We describe current understanding of the complexities of HLA association for RA. Linkage and small-scale association studies prior to 2007 provided convincing evidence for only one more RA susceptibility locus, PTPN22. Major breakthroughs in high-throughput genotyping, and systematic discovery and mapping of hundreds of thousands of single nucleotide polymorphisms (SNPs) led to large-scale genome-wide association studies used for the first time for RA in 2007. Widespread utilization of this approach has had a dramatic impact on our knowledge of the susceptibility loci for RA, such that over 100 risk variants have now been robustly identified. We present an overview of these studies and the loci that have been identified. We consider how this knowledge is contributing to a greater understanding of the aetiology and pathology of the disease, and in turn how this can influence management of patients presenting with an inflammatory arthritis. We consider some of the unanswered questions and the approaches that will need to be taken to address them.

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